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- PDB-7ars: The de novo designed hybrid alpha/beta-miniprotein (with Se-Methi... -

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Basic information

Entry
Database: PDB / ID: 7ars
TitleThe de novo designed hybrid alpha/beta-miniprotein (with Se-Methionine)
Componentsalpha/beta-peptide
KeywordsDE NOVO PROTEIN / alpha/beta-peptide / foldamer
Function / homologytrifluoroacetic acid
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsBejger, M. / Fortuna, P. / Drewniak-Switalska, M. / Rypniewski, W. / Berlicki, L.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreDEC-2016/21/B/ST5/00269 Poland
CitationJournal: Chem.Commun.(Camb.) / Year: 2021
Title: A computationally designed beta-amino acid-containing miniprotein.
Authors: Bejger, M. / Fortuna, P. / Drewniak-Switalska, M. / Plewka, J. / Rypniewski, W. / Berlicki, L.
History
DepositionOct 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha/beta-peptide
B: alpha/beta-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4314
Polymers8,2932
Non-polymers1382
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-16 kcal/mol
Surface area4360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.089, 35.481, 41.919
Angle α, β, γ (deg.)90.000, 111.240, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-101-

TFA

21A-224-

HOH

31B-125-

HOH

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Components

#1: Protein/peptide alpha/beta-peptide


Mass: 4146.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium chloride hexahydrate 0.1 M Tris pH 8.5 20 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 24712 / % possible obs: 97.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 18.1 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.61
Reflection shellResolution: 1.15→1.22 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.95 / Num. unique obs: 3610 / CC1/2: 0.91 / % possible all: 88.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: not deposited

Resolution: 1.15→39.07 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.201 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 1001 4.1 %RANDOM
Rwork0.1745 ---
obs0.1763 23711 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 397.64 Å2 / Biso mean: 20.083 Å2 / Biso min: 10.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å20.32 Å2
2---2.34 Å20 Å2
3---1.68 Å2
Refinement stepCycle: final / Resolution: 1.15→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms508 0 8 102 618
Biso mean--32.49 33.75 -
Num. residues----62
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.014732
X-RAY DIFFRACTIONr_bond_other_d0.0060.018718
X-RAY DIFFRACTIONr_angle_refined_deg2.5581.747962
X-RAY DIFFRACTIONr_angle_other_deg1.5691.721693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.819574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.38724.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7115141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.652154
X-RAY DIFFRACTIONr_chiral_restr0.1480.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02701
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02123
X-RAY DIFFRACTIONr_rigid_bond_restr7.96231444
LS refinement shellResolution: 1.15→1.175 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.355 56 -
Rwork0.285 1334 -
obs--75.54 %

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